sequence quality in eprimer3
Peter Rice
pmr at ebi.ac.uk
Thu Jun 5 08:32:59 UTC 2003
Guy Bottu wrote:
> I am afraid that the EMBOSS "wrapper" program eprimer3 does not handle the base
> assignment qualities, even if the manual briefly mentions it. Actually, EMBOSS
> does not handle Staden experiment files. If you ask seqret to write
> experiment::xxx it writes a sequence in the now obsolete Staden format.
> (let's not blame the developers, it is such a monumental task to implement
> everything...)
Not too difficult. I believe the Staden experiment file format is
similar to EMBL.
We don't see the Staden format as obsolete (and only GCG seem to call it
"Staden" - it's just a nice name for a plain sequence format.
> You might install primer through its "native" interface, using the
> primer3_www.cgi script. This is more rich than EMBOSS, but is of course
> "featureless" (no access to personal files on the server). You still will have
> to extract "manually" the content of the AV lines and copy-and-paste in the
> "Sequence Quality" box.
We could try adding the base qualities - yet more options for eprimer3.
How many users would like this added in EMBOSS?
Peter
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